Replaced the bearing which really helped with extruder clicking.
The shorted pins were a problem with the extruder PCB, and the other problem was that the socket that holds the extruder cable end was a little warped, so the cable wouldn't stay in place.
The main problem I have now is that the support material is completely stuck to the print. I was able to improve other aspects of "smushing" by tightening the Z-Axis, increasing First Layer Gap, and slowing/extending retraction.
Temperature seems to be happy at around 245 degrees.
I'm a bit confused as to where to go next, since there is no setting to add a gap above the support material, which I imagine would solve the problem I'm having.
The only other components I can think that would be an issue are the perforated plate and motherboard, although that is a bit out of my budget at this point. Even if there is a hacky solution that would be more ideal for now.
Any ideas or pointers would be greatly appreciated :-)
Zortrax advised to go back to the original hotend, but I'm hesitant to do that since it's so crusty and the nozzle is kind of beaten up.